adilinden:
Seems to be easier with the Variants folder now to implement a different mapping, need to look into that more.
I will have to figure that one out. It seems one can define everything there is to a custom board and place it in the sketches folder. No need to modify any of the original Arduino distributed file. I sure hope that is how it works.
That's the theory. In practice some libraries make assumptions about the pin mapping based on microcontroller type. The SD library has its own pin mapping tables, for the ATmega1284 it assumes the Sanguino pin mapping. 
I've forked the Arduino software on Github to get the my mapping used for the SD library. I've tried to replace this mapping table by the Variants one, but haven't yet succeeded. It seems that the pin mapping tables in Variants are only included when compiling the sketch.ino file, and not when associated libraries are compiled (see the #ifdef ARDUINO_MAIN compiler conditional in the standard pins_arduino.h files).